Intersecting evolutionary and medical genetics to understand human brain development and disease

Abstract

There is an increasing appreciation for the role of non-coding regions of the genome in normal neurodevelopment and disease. Although noncoding regions of the genome that are conserved across species appear to contribute disproportionately to neurodevelopmental conditions such as Autism Spectrum Disorder (ASD) the relative importance of different classes of noncoding sequences for human neuropsychiatric disease is not known. We sequenced 3 classes of conserved non-coding regions of the genome - Conserved Neural Enhancers (CNEs), Human Accelerated Regions (HARs), and validated Vista Enhancers (VEs) - and assessed their contribution to ASD risk in a cohort of 6,464 ASD patients and family members through targeted sequencing. We find that rare mutations in both HARs and VEs contribute to ASD risk in a recessive autosomal or X-linked manner, while the most population-constrained elements, CNEs, lack a detectable recessive contribution in our cohort. We validated these results in 8,186 additional individuals using whole genome sequencing datasets from Simon Simplex Collection, where we observed a female specific enrichment in rare biallelic HAR mutations. Capture-based Massively Parallel Reporter Assay (caMPRA) experiments demonstrated that many of the HARs, CNEs, and VEs possess enhancer activity, and rare variants can lead to striking changes in regulatory function of the elements. Analysis of the genomic distribution of these elements shows that they cluster within the introns of highly dosage-sensitive genes, where slight changes in expression level are expected to produce phenotypic consequences. Finally, saturation mutagenesis of two HARs near the highly dosage sensitive ASD/ID gene IL1RAPL1 demonstrated that these two HARs possess functional transcription factor binding sites (TFBS), a subset of which are changed or gained in the human lineage. Surprisingly, these newly formed TFBS are disrupted in several ASD patients. Together we characterize how conserved elements are enriched for function in neurodevelopment, and how human specific changes in these regions can create new TFBS that are vulnerable to damaging variants. Finally, the functional redundancy of important enhancers may permit them to be less constrained in the genome with essential contributions to brain development only revealed in a recessive manner.